Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 185143.33 
• Atom Count: 14241 
• Residue Count: 1588 
• Unique protein chains: 1

1XPM

Crystal Structure of Staphylococcus aureus HMG-COA Synthase with HMG-CoA and Acetoacetyl-COA and Acetylated Cysteine

• DOI: 10.2210/pdb1XPM/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus (strain MW2)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2004-10-08 Released: 2004-11-02 
• Deposition Author(s): Theisen, M.J., Misra, I., Saadat, D., Campobasso, N., Miziorko, H.M., Harrison, D.H.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.226 
• R-Value Work: 0.210 

Literature

3-hydroxy-3-methylglutaryl-CoA synthase intermediate complex observed in "real-time"

Theisen, M.J., Misra, I., Saadat, D., Campobasso, N., Miziorko, H.M., Harrison, D.H.T.

(2004) Proc.Natl.Acad.Sci.USA 47: 16442-16447

• PubMed: 15498869 
• DOI: 10.1073/pnas.0405809101
• Primary Citation of Related Structures:  
  1XPL, 1XPK


• PubMed Abstract: 
  

The formation of carbon-carbon bonds via an acyl-enzyme intermediate plays a central role in fatty acid, polyketide, and isoprenoid biosynthesis. Uniquely among condensing enzymes, 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGS) catalyzes the formation of a carbon-carbon bond by activating the methyl group of an acetylated cysteine. This reaction is essential in Gram-positive bacteria, and represents the first committed step in human cholesterol biosynthesis. Reaction kinetics, isotope exchange, and mass spectroscopy suggest surprisingly that HMGS is able to catalyze the "backwards" reaction in solution, where HMG-CoA is cleaved to form acetoacetyl-CoA (AcAc-CoA) and acetate. Here, we trap a complex of acetylated HMGS from Staphylococcus aureus and bound acetoacetyl-CoA by cryo-cooling enzyme crystals at three different times during the course of its back-reaction with its physiological product (HMG-CoA). This nonphysiological "backwards" reaction is used to understand the details of the physiological reaction with regards to individual residues involved in catalysis and substrate/product binding. The structures suggest that an active-site glutamic acid (Glu-79) acts as a general base both in the condensation between acetoacetyl-CoA and the acetylated enzyme, and the hydrolytic release of HMG-CoA from the enzyme. The ability to trap this enzyme-intermediate complex may suggest a role for protein dynamics and the interplay between protomers during the normal course of catalysis.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
3-hydroxy-3-methylglutaryl CoA synthase	A, B, C, D	396	Staphylococcus aureus (strain MW2)	Mutation(s): 0  Gene Names: mvaS
Find proteins for A0A0H3K1U2 (Staphylococcus aureus (strain MW2)) Go to UniProtKB:  A0A0H3K1U2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CAA	A, B, C, D	ACETOACETYL-COENZYME A C25 H40 N7 O18 P3 S OJFDKHTZOUZBOS-CITAKDKDSA-N
HMG	A, B, C, D	3-HYDROXY-3-METHYLGLUTARYL-COENZYME A (S)-HMG-COA C27 H39 N7 O20 P3 S CABVTRNMFUVUDM-VRHQGPGLSA-I
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCY	A, B, C, D	L-PEPTIDE LINKING	C5 H9 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.226 
• R-Value Work: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 65.119	α = 90.00
b = 118.774	β = 90.08
c = 121.304	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
DENZO	data reduction
BEAST	phasing
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-08 
• Released Date: 2004-11-02 
• Deposition Author(s): Theisen, M.J., Misra, I., Saadat, D., Campobasso, N., Miziorko, H.M., Harrison, D.H.T.

Revision History 

• Version 1.0: 2004-11-02
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description